1. Field of the Invention
This invention relates to modulating gene expression associated with a disease or disorder, and identifying targets for therapeutic intervention that are genes differentially expressed in cells or tissues expressing a disease or disorder.
2. Background of the Invention
The completion of the Human Genome Project revealed the presence of about 35,000 genes in the human genome, a number smaller than anticipated (Lander et al., 2001, Nature 409: 860-921; International Human Genome Consortium, 2004, Nature 431: 931-945). As a consequence, the art has come to recognize the crucial part gene regulation plays in expressing a wide variety of phenotypes, which phenotypes may be produced by differential expression of genes in different tissues and under different developmental pathways.
The art has long recognized (see, Stent & Calendar, 1978, MOLECULAR GENETICS, 2d ed., Chapter 20, W.H. Freeman & Co.: San Francisco) the existence of cis and trans genetic elements for gene regulation, comprising genetic sequences in cis typically associated with promoter elements in one or a plurality of genes, particularly in coordinately-regulated genes, and regulatory proteins provided in trans that mediate gene regulation of promoters associated with their cognate cis elements.
In mammalian cells, one such element is a 23 base pair regulatory sequence in their promoter regions known as the Neuron Restrictive Silencing Element (NRSE)(Maue et al., 1990, Neuron 4: 223-31; Mori et al., 1990, Neuron 4: 583-94;). This element is found in the promoter regions of about 1800 genes in the mouse and human genomes (Maue et al., 1990, Id.; Mori et al., 1990, Id.; Bruce et al., 2004, Proc Natl Acad Sci USA 101: 10458-63). As a 23 base pair sequence, this element is unlikely to occur randomly, and genes with NRSEs are repressed both outside and inside the nervous system by the transcription factor Neural Restrictive Silencing Factor/Repressor of Expression of Sodium Type II (NRSF, also referred to as REST)(Chong et al., 1995, Cell 80: 949-57). Neuronal gene expression regulated by NRSF plays an important role in normal development and maintenance of neuronal phenotypes (Chong et al., 1995, Id.; Schoenherr & Anderson, 1995, Science 267: 1360-3; Chen et al., 1998, Nat. Genet. 20: 136-42; Timmusk et al., 1999, J. Biol Chem 274: 1078-84; Zuccato et al., 2003, Nat. Genet 35: 76-83), but there has been less understanding about the potential contribution of transcriptional regulation of neuronal gene expression by NRSF to pathological processes, including diseases of the nervous system and other systemic diseases.
One example of a gene regulated by NRSE/NRSF is Brain Derived Neurotrophic Factor (BDNF) and its tyrosine kinase receptor trkB (Timmusk et al., 1999, Id.). BDNF and trkB signaling have been implicated in a variety of neuronal and neural circuit phenomena in the developing and adult brain including axon sprouting, synapse formation, development of recurrent neuronal circuits that promote hyper-excitability, and long-term potentiation (LTP)(Timmusk & Metsis, 1994, Neurochem. Intl. 25: 11-15), and conditional genetic knockouts of the NRSF target genes BDNF and trkB potently modify progression of kindling, a phenomenon of activity-dependent neural plasticity and an animal model of epilepsy (Kokaia et al., 1995, Exp Neurol 133: 215-24; He et al., 2004, Neuron 43: 31-42). In addition, recent studies have demonstrated that BDNF and trkB are also important in phenomena involving cells of epithelial origin outside the nervous system, such as the acquisition of metastatic potential and anoikis in cancer cells (Belyaev et al., 2004, J. Biol. Chem. 279: 556-561; Douma et al., 2004, Nature 430: 1034-9; Pearse et al., 2005, Blood 105: 4429-36). Potential target genes regulated by NRSE/NRSF include MDR3/MRP3 (cancer), MTA1, DCC (cancer), Netrin, beta-catenin (cancer), BDNF and TrkB (metastasis and anoikis, sleep apnea, epilepsy, pain), and atrial natriuretic peptide (cardiac hypertrophy/myocardial infarction)(Mazumdar et al., 2001, Nat. Cell Biol. 3: 30-37; Wood et al., 2003, J. Molec. Biol. 334: 863-74; Mimezami et al., 2003, Curr Biol 13: 1234-9; Bruce et al., 2004, Id.; Kim et al., 2005, Nat Struct Mol Biol 12: 423-8; Westbrook et al., 2005, Cell 121: 837-848).
A variety of metabolic intermediates act as small-molecule regulators of gene expression co-repressors and co-activators, thereby linking energy availability to chromatin structure and transcriptional output (Peterson, 2000, FEBS Lett 476: 68-72; Brown et al., 2000, Trends Biochem Sci 25: 15-9; Guarente & Picard, 2005, Cell 120: 473-82). For example, glycolysis-derived NADH is known to be an allosteric regulator of the transcriptional corepressor CtBP which suggests that CtBP could act as a redox sensor that directly integrates metabolic demands with gene expression (Zhang et al., 2002, Science 295: 1895-7). These relationships suggest a link between cellular energy states, particularly redox potential reflected in the amount of NAD and NADH in the cell, and gene expression regulation. However, there is no evidence in the art that cellular metabolism or energetics can modulate expression of NRSE/NRSF regulated genes.
There is this generally a need in the art to identify methods for modulating gene expression, particularly metabolic methods for modulating gene expression, for genes and phenotypes associated with a disease or disorder, as a way to prevent development of the disease or disorder or develop a treatment for the disease or disorder, as well as methods for identifying targets for therapeutic intervention.